{"id":959,"date":"2022-03-17T15:52:16","date_gmt":"2022-03-17T14:52:16","guid":{"rendered":"https:\/\/pgtb.fr\/?page_id=959"},"modified":"2024-12-10T16:40:11","modified_gmt":"2024-12-10T15:40:11","slug":"sequenceurs-oxford-nanopore","status":"publish","type":"page","link":"https:\/\/pgtb.fr\/en\/sequenceurs-oxford-nanopore\/","title":{"rendered":"S\u00e9quenceurs Oxford Nanopore"},"content":{"rendered":"<p class=\"wp-block-paragraph\">La plateforme a investi dans une machine de calculs puissante pour contr\u00f4ler \u00e0 la fois le MinION et le P2 solo et ainsi assumer la mont\u00e9e en d\u00e9bit des flow cells PromethION.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">La plateforme b\u00e9n\u00e9ficie ainsi d\u2019une grande capacit\u00e9 de calcul pour le basecalling haute pr\u00e9cision, l\u2019alignement en direct ainsi que l\u2019Adaptive Sampling.<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img data-recalc-dims=\"1\" fetchpriority=\"high\" decoding=\"async\" width=\"750\" height=\"504\" data-attachment-id=\"1978\" data-permalink=\"https:\/\/pgtb.fr\/en\/sequenceurs-oxford-nanopore\/2ont\/\" data-orig-file=\"https:\/\/i0.wp.com\/pgtb.fr\/wp-content\/uploads\/2024\/03\/2ont.png?fit=806%2C542&amp;ssl=1\" data-orig-size=\"806,542\" data-comments-opened=\"1\" data-image-meta=\"{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}\" data-image-title=\"2ont\" data-image-description=\"\" data-image-caption=\"\" data-large-file=\"https:\/\/i0.wp.com\/pgtb.fr\/wp-content\/uploads\/2024\/03\/2ont.png?fit=750%2C504&amp;ssl=1\" src=\"https:\/\/i0.wp.com\/pgtb.fr\/wp-content\/uploads\/2024\/03\/2ont.png?resize=750%2C504&#038;ssl=1\" alt=\"\" class=\"wp-image-1978\" \/><figcaption class=\"wp-element-caption\">S\u00e9quenceurs Oxford Nanopore Technologies : MinION (\u00e0 gauche) et P2 solo (\u00e0 droite)<\/figcaption><\/figure>\n\n\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><tbody><tr><td><strong><u>Reads Haute Qualit\u00e9<\/u><\/strong>&nbsp; &#8211;&nbsp; <strong><u>HERRO<\/u><\/strong> (Haplotype-aware ERRor cOrrection)<br>&nbsp;<br>Un outil r\u00e9cent, HERRO (<a href=\"https:\/\/github.com\/lbcb-sci\/herro\">https:\/\/github.com\/lbcb-sci\/herro<\/a>), permet une \u00ab\u00a0auto-correction\u00a0\u00bb des reads nanopore.<br>Il s\u2019agit de la m\u00eame \u00e9quipe qui avait d\u00e9j\u00e0 d\u00e9velopp\u00e9 des outils tr\u00e8s largement utilis\u00e9s comme Racon et Pilon.<br>&nbsp;<br>Les reads corrig\u00e9s par HERRO sont ainsi de tr\u00e8s haute qualit\u00e9 (&gt;&gt; Q30).<br>&nbsp;<br>Cette correction de reads s&rsquo;applique uniquement aux reads au-del\u00e0 de 5 Kb.<br>L&rsquo;application premi\u00e8re est donc l&rsquo;assemblage de g\u00e9nomes.<br>&nbsp;<br>La PGTB dispose des ressources informatiques ad\u00e9quates pour vous fournir ces reads corrig\u00e9s (format fasta) en plus des fastq bruts.<br>&nbsp;<br><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.05.18.594796v1\">https:\/\/www.biorxiv.org\/content\/10.1101\/2024.05.18.594796v1<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<p class=\"has-normal-font-size wp-block-paragraph\"><strong>Kits<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>LSK114 <\/strong>: maximum de d\u00e9bit, barcoding possible en ligation. Pour s\u00e9quen\u00e7age shotgun, m\u00e9tag\u00e9nomique et amplicons<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>RBK114 <\/strong>: maximum de rapidit\u00e9, minimum d\u2019ADN et minimum de co\u00fbt. Barcoding possible par tagmentation. Pour s\u00e9quen\u00e7age shotgun et m\u00e9tag\u00e9nomique<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>RNA Direct<\/strong> : S\u00e9quen\u00e7age d\u2019ARNm natifs. Acc\u00e8s aux isoformes et aux bases modifi\u00e9es<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>cDNA <\/strong>: S\u00e9quen\u00e7age stranded des ARNm. Acc\u00e8s aux isoformes<\/p>\n\n\n\n<p class=\"has-normal-font-size wp-block-paragraph\"><strong>Flow Cells &amp; d\u00e9bits<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Plusieurs facteurs impactent la quantit\u00e9 de donn\u00e9es g\u00e9n\u00e9r\u00e9es quel que soit le type de flow cell&nbsp;:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Qualit\u00e9 \/ puret\u00e9 de l\u2019ADN (ARN)<\/li>\n\n\n\n<li>Taille des mol\u00e9cules<\/li>\n\n\n\n<li>Fraicheur des kits &amp; flow cell<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Flongle R10<\/strong> : &lt; 500Mb &#8211;&nbsp; Flow cell bas d\u00e9bit. Id\u00e9al pour r\u00e9aliser des tests \u00e0 bas co\u00fbt.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>MinION R10<\/strong>&nbsp;: 3 \u2013 10Gb<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>PromethION R10<\/strong> : 40 \u2013 100Gb<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img data-recalc-dims=\"1\" decoding=\"async\" width=\"750\" height=\"497\" data-attachment-id=\"1977\" data-permalink=\"https:\/\/pgtb.fr\/en\/sequenceurs-oxford-nanopore\/3_fcs\/\" data-orig-file=\"https:\/\/i0.wp.com\/pgtb.fr\/wp-content\/uploads\/2024\/03\/3_fcs.jpg?fit=3440%2C2280&amp;ssl=1\" data-orig-size=\"3440,2280\" data-comments-opened=\"1\" data-image-meta=\"{&quot;aperture&quot;:&quot;1.8&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;realme C3&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;1710851362&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;4.05&quot;,&quot;iso&quot;:&quot;162&quot;,&quot;shutter_speed&quot;:&quot;0.02&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;1&quot;}\" data-image-title=\"3_fcs\" data-image-description=\"\" data-image-caption=\"\" data-large-file=\"https:\/\/i0.wp.com\/pgtb.fr\/wp-content\/uploads\/2024\/03\/3_fcs.jpg?fit=750%2C497&amp;ssl=1\" src=\"https:\/\/i0.wp.com\/pgtb.fr\/wp-content\/uploads\/2024\/03\/3_fcs.jpg?resize=750%2C497&#038;ssl=1\" alt=\"\" class=\"wp-image-1977\" \/><figcaption class=\"wp-element-caption\">Flow cells Oxford Nanopore Technologies : Flongle &#8211; MinION &#8211; PromehION (de gauche \u00e0 droite)<\/figcaption><\/figure>","protected":false},"excerpt":{"rendered":"<p>La plateforme a investi dans une machine de calculs puissante pour contr\u00f4ler \u00e0 la fois le MinION et le P2 solo et ainsi assumer la mont\u00e9e en d\u00e9bit des flow cells PromethION. La plateforme b\u00e9n\u00e9ficie ainsi d\u2019une grande capacit\u00e9 de calcul pour le basecalling haute pr\u00e9cision, l\u2019alignement en direct ainsi que l\u2019Adaptive Sampling. Reads Haute<a class=\"more-link\" href=\"https:\/\/pgtb.fr\/en\/sequenceurs-oxford-nanopore\/\">Continue reading <span class=\"screen-reader-text\">\u00ab\u00a0S\u00e9quenceurs Oxford Nanopore\u00a0\u00bb<\/span><\/a><\/p>","protected":false},"author":216247060,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_crdt_document":"","advanced_seo_description":"","jetpack_seo_html_title":"","jetpack_seo_noindex":false,"footnotes":""},"class_list":["post-959","page","type-page","status-publish","hentry","entry"],"jetpack_likes_enabled":true,"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/PdFmHm-ft","jetpack-related-posts":[],"_links":{"self":[{"href":"https:\/\/pgtb.fr\/en\/wp-json\/wp\/v2\/pages\/959","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pgtb.fr\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pgtb.fr\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pgtb.fr\/en\/wp-json\/wp\/v2\/users\/216247060"}],"replies":[{"embeddable":true,"href":"https:\/\/pgtb.fr\/en\/wp-json\/wp\/v2\/comments?post=959"}],"version-history":[{"count":22,"href":"https:\/\/pgtb.fr\/en\/wp-json\/wp\/v2\/pages\/959\/revisions"}],"predecessor-version":[{"id":2361,"href":"https:\/\/pgtb.fr\/en\/wp-json\/wp\/v2\/pages\/959\/revisions\/2361"}],"wp:attachment":[{"href":"https:\/\/pgtb.fr\/en\/wp-json\/wp\/v2\/media?parent=959"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}